The development of the digital economy provides new pathways to support urban resilience enhancement, particularly for enhancing the resilience of cities in river basins. Based on panel data from 146 cities in river basin in China from 2011 to 2023, this paper constructs an evaluation index system for the level of digital economy development, measures urban resilience using a super-efficiency SBM model, and empirically examines the impact of the digital economy on urban resilience in the Yellow River, Yangtze River, and Pearl River Basins using a two-way fixed effects model. Furthermore, it tests the mediating role of virtual agglomeration in the impact of the digital economy on urban resilience. The results show that the development of the digital economy significantly enhances the resilience of cities in the full sample, as well as in the Yangtze River and Pearl River Basins, while its positive effects on the resilience in cities in the Yellow River Basin are insignificant. The impact of the digital economy on urban resilience varies according to differences in urban innovation capacity and fiscal self-sufficiency, with stronger enabling effects observed in cities with higher levels of innovation and fiscal independence. Moreover, the promoting effect of the digital economy on urban resilience shows significant spatial heterogeneity across the upper, middle, and lower reaches of the three river basins. The development of the digital economy enhances urban resilience overall and across the three basins by promoting virtual agglomeration. Accordingly, this paper proposes the following policy implications: strengthening the digital economy in the three river basins according to local conditions, consolidating the foundations for innovation capacity and fiscal support, and reinforcing virtual space infrastructure to improve urban resilience.